I just rooted my NC. If B&N comes out with an update and my NC updates automatically will this cause problems? If so what kinds of problems? I briefly looked into turning off the auto update but it seems a bit complicated for me who is not a techie.

Unknown. Because you are rooted, it may not update, it may update but abort the install, it may try to update and not apply cleanly, it might update and you'd lose root, it may cause reboot loops. However, in all cases you could do a reset of your nook to 1.00, re-update to a known version and reroot and then check forums for info on updating/turning off updates. If you do a backup with one of the backup apps or a nandroid backup you could get your apps and data back more quickly.